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project.yaml
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project.yaml
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version: "3.0"
expectations:
population_size: 10000
actions:
generate_study_population_ae:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ae
outputs:
highly_sensitive:
cohort: output/input_ae.csv
generate_ae_count:
run: python:latest python analysis/ae_count.py
needs: [generate_study_population_ae]
outputs:
moderately_sensitive:
count: output/ae_count.json
hospital_count: output/hospital_admission_count.json
generate_study_population_descriptives:
run: cohortextractor:latest generate_cohort --study-definition study_definition_descriptives
outputs:
highly_sensitive:
cohort: output/input_descriptives.csv
generate_study_population_alternative:
run: cohortextractor:latest generate_cohort --study-definition study_definition_alternative
outputs:
highly_sensitive:
cohort: output/input_alternative.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_results:
run: python:latest python analysis/generate_results.py
needs: [generate_study_population, generate_study_population_descriptives]
outputs:
moderately_sensitive:
num_patients: output/num_patients.json
ae_attendance_count_dict: output/num_ae_attendances.json
hosp_dict: output/emergency_hospitalisation.json
ae_dict: output/ae.json
any_ae_dict: output/ae_any.json
all_ae_dict: output/ae_all.json
discharge_csv: output/discharge_destination.csv
performance_dict: output/model_performance_updated.json
sensitivity_dict: output/sensitivity.json
model_csvs: output/model_*.csv
venn: output/venn.jpeg
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/results.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_study_population, generate_study_population_descriptives]
outputs:
moderately_sensitive:
notebook: output/results.html
generate_notebook_alternative:
run: jupyter:latest jupyter nbconvert /workspace/analysis/analysis.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_study_population_alternative]
outputs:
moderately_sensitive:
notebook: output/analysis.html